fix: fix app update command and duplicated apps (backport #3931)

[mergify]

This is an automatic backport of pull request #3931 done by Mergify.

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[codecov]

Codecov Report

Attention: 13 lines in your changes are missing coverage. Please review.

Comparison is base (67c39ec) 24.77% compared to head (adcd42a) 24.78%.

Additional details and impacted files

@@               Coverage Diff                @@
##           release/v28.x.y    #3938   +/-   ##
================================================
  Coverage            24.77%   24.78%           
================================================
  Files                  296      296           
  Lines                24905    24901    -4     
================================================
  Hits                  6171     6171           
+ Misses               18168    18164    -4     
  Partials               566      566           

Files	Coverage Δ
ignite/cmd/cmd.go	5.82% <0.00%> (-0.13%)	⬇️
ignite/cmd/plugin.go	28.46% <0.00%> (+0.41%)	⬆️